FastQC Summary

Summary statistics for all libraries
Filename Total Flagged As Poor Quality Sequence Length %GC
G1_KI_R1_clean.fq.gz 9,633,848 0 30-150 45
G1_KI_R2_clean.fq.gz 9,633,848 0 30-150 45
G1_KI_singletons_clean.fq.gz 7,415,483 0 30-150 43
G2_KI_R1_clean.fq.gz 7,490,193 0 30-150 43
G2_KI_R2_clean.fq.gz 7,490,193 0 30-150 44
G2_KI_singletons_clean.fq.gz 9,151,523 0 30-150 43
G3_KI_R1_clean.fq.gz 6,247,947 0 30-150 44
G3_KI_R2_clean.fq.gz 6,247,947 0 30-150 44
G3_KI_singletons_clean.fq.gz 9,081,708 0 30-150 44
G4_KI_R1_clean.fq.gz 7,242,293 0 30-150 44
G4_KI_R2_clean.fq.gz 7,242,293 0 30-150 44
G4_KI_singletons_clean.fq.gz 8,661,390 0 30-150 45
G5_KI_R1_clean.fq.gz 5,731,056 0 30-150 43
G5_KI_R2_clean.fq.gz 5,731,056 0 30-150 43
G5_KI_singletons_clean.fq.gz 9,698,982 0 30-150 42
G6K_CDNJBANXX_R1_clean.fq.gz 70,903,097 0 30-125 45
G6K_CDNJBANXX_R2_clean.fq.gz 70,903,097 0 30-125 45
G6K_CDNJBANXX_singletons_clean.fq.gz 42,315 0 30-125 45
G6T_CDNJBANXX_R1_clean.fq.gz 68,246,684 0 30-125 47
G6T_CDNJBANXX_R2_clean.fq.gz 68,246,684 0 30-125 47
G6T_CDNJBANXX_singletons_clean.fq.gz 44,582 0 30-125 47
G7K_CDNJBANXX_R1_clean.fq.gz 73,079,277 0 30-125 46
G7K_CDNJBANXX_R2_clean.fq.gz 73,079,277 0 30-125 46
G7K_CDNJBANXX_singletons_clean.fq.gz 77,840 0 30-125 46
G8_KI_R1_clean.fq.gz 8,192,568 0 30-150 44
G8_KI_R2_clean.fq.gz 8,192,568 0 30-150 44
G8_KI_singletons_clean.fq.gz 8,723,253 0 30-150 44

Read Totals

Library Sizes ranged between 42,315 and 73,079,277 reads.

Read totals for each library. Duplicated reads are conventionally an high overestimate at this point.

FastQC Summary

Summary of FastQC flags for each parameter

Per Base Sequence Quality

Heatmap showing mean base qualities for each library

Per Sequence Quality Scores

Heatmap showing mean sequence qualities for each library

Per Base Sequence Content

Heatmap of summed base distributions along each read

Per Sequence GC Content

GC Content Heatmap normalised to theoretical GC content in the Hsapiens Transcriptome

GC Content Distributions for all reads showing theoretical GC content from the Hsapiens Transcriptome

Sequence Length Distribution

Sequence Duplication Levels

Adapter Content

Universal Adapter Content

Overrepresented Summary

- error -

Overrepresented_sequences missing from G1_KI_R2_clean.fq.gz Overrepresented_sequences missing from G4_KI_R2_clean.fq.gz Overrepresented_sequences missing from G8_KI_R2_clean.fq.gz Quitting from lines 188-189 (ngsReports_Fastqc.Rmd) Error: Aesthetics must be either length 1 or the same as the data (24): key

Overrepresented Sequences

## Overrepresented_sequences missing from G1_KI_R2_clean.fq.gz
## Overrepresented_sequences missing from G4_KI_R2_clean.fq.gz
## Overrepresented_sequences missing from G8_KI_R2_clean.fq.gz
## `summarise()` regrouping output by 'Sequence' (override with `.groups` argument)
Summary of the most overrepresented sequences in all files. A maximum of 30 sequences are shown
Sequence Total Present In Overall Percentage Max_Percentage Possible_Source
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 2,895,530 15 0.51118847% 4.266778% No Hit
GTCCGAAGGTGCAGCTACCACGGGCCTGGCCGCAAGCAAGTGTATCAGCA 533,564 2 0.09419753% 0.519317% No Hit
CTCCCCTCTGCCCAGCATGTTTCCACATTCTACATTTCTAAGTGAATGGC 504,275 2 0.08902673% 0.475174% No Hit
GTCAGACTTCTAGCTCTAGCAAGGACTCCTGCACTAAGCTTCAGCCATGA 325,104 2 0.05739516% 0.299131% No Hit
CCGATGTTTTCAGAGGTGCCTCTGCATGGTCCGAAGGTGCAGCTACCACG 301,849 2 0.05328963% 0.261275% No Hit
CAGACTTCTAGCTCTAGCAAGGACTCCTGCACTAAGCTTCAGCCATGAGG 234,391 2 0.04138033% 0.218089% No Hit
GTGGAAAGAAGGTTAGGTTGACACCGGCAAATATGACGCCAAATTGAATT 193,964 2 0.03424318% 0.158729% No Hit
GTCCCGATGTTTTCAGAGGTGCCTCTGCATGGTCCGAAGGTGCAGCTACC 144,144 1 0.02544776% 0.197243% No Hit
GGGGATTCTATGGGGACTACTATGCGGTGATCTACTTCTAGCAGACGAAG 131,053 1 0.02313662% 0.179330% No Hit
CTCGACGTCCGTGTCGCCTCCTGCGACGGCGACGACTGAGGCTGCGGCTC 128,276 1 0.02264636% 0.187959% No Hit
CCTCGACGTCCGTGTCGCCTCCTGCGACGGCGACGACTGAGGCTGCGGCT 118,522 1 0.02092435% 0.173667% No Hit
GGATCCTCTTCCTTCTCTTTACCATCTTTTTGGTCTTCTACCAAGCTGCT 117,254 1 0.02070049% 0.160448% No Hit
CGATGTTTTCAGAGGTGCCTCTGCATGGTCCGAAGGTGCAGCTACCACGG 115,112 1 0.02032233% 0.157517% No Hit
AGCCCATCAAGGACAGGTGGCGCTCCAGCTGCACAGAGCTCAAAAGGCAA 108,354 1 0.01912925% 0.158768% No Hit
CGGGGAACTGCCAGGAGAAAAAGGATTGGCCATCAAGATGTAGGTTCTGG 95,991 1 0.01694664% 0.135383% No Hit
CGGGGAACTGCCAGGAGAAAATGGATTGGCCATCAAGATGTAGGTTCTGG 91,646 1 0.01617955% 0.125406% No Hit
GGGGATTGTTGATTTCGTCTATAAGATAAAGGATGCGGAGGGAGGGGAGG 88,539 1 0.01563103% 0.121155% No Hit
GTTCGGCTTCCAAGACGCAGCATCACCAATCATAGAAGAGCTTTTACACT 86,685 1 0.01530372% 0.118618% No Hit
GGACAGGTGGCGCTCCAGCTGCACAGAGCTCAAAAGGCAAAGCACCATCT 82,994 1 0.01465209% 0.121609% No Hit
CCCACAGTAAACAGGAAAATAAAACCAAGAGCTCAGAGTATGGCAGCATC 81,660 1 0.01441658% 0.115171% No Hit
CCCCTCTGCCCAGCATGTTTCCACATTCTACATTTCTAAGTGAATGGCTC 79,546 1 0.01404337% 0.108849% No Hit
CTCCGACCGTGTCTGCGACCTCTTCTTCTGCCATGGCGCCTTCCCTTCTT 75,185 1 0.01327346% 0.110167% No Hit
CCCCACAGTAAACAGGAAAATAAAACCAAGAGCTCAGAGTATGGCAGCAT 71,370 1 0.01259995% 0.100659% No Hit
AACTTCCAGCTTCTCAGATATCTCATGGTCCTGGGCGTGCCCATTTGCAG 68,170 4 0.01203501% 0.248246% No Hit
TTCTCAGATATCTCATGGTCCTGGGCGTGCCCATTTGCAGCAGCTGAGAG 57,064 4 0.01007431% 0.210368% No Hit
TTCCAGCTTCTCAGATATCTCATGGTCCTGGGCGTGCCCATTTGCAGCAG 54,223 4 0.00957275% 0.198894% No Hit
AGAAGTTGCAGGCAACTTCCAGCTTCTCAGATATCTCATGGTCCTGGGCG 52,706 4 0.00930493% 0.194512% No Hit
AGGCAACTTCCAGCTTCTCAGATATCTCATGGTCCTGGGCGTGCCCATTT 48,854 4 0.00862488% 0.181133% No Hit
GTGCCCATTTGCAGCAGCTGAGAGTTCCAAGTTGGCAGGTCCCGATGTTT 37,798 3 0.00667301% 0.175903% No Hit
AGCTTCTCAGATATCTCATGGTCCTGGGCGTGCCCATTTGCAGCAGCTGA 35,573 3 0.00628020% 0.163604% No Hit

Session Information

R version 3.6.1 (2019-07-05)

Platform: x86_64-w64-mingw32/x64 (64-bit)

locale: LC_COLLATE=English_Australia.1252, LC_CTYPE=English_Australia.1252, LC_MONETARY=English_Australia.1252, LC_NUMERIC=C and LC_TIME=English_Australia.1252

attached base packages: parallel, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: readr(v.1.4.0), stringr(v.1.4.0), magrittr(v.2.0.1), scales(v.1.1.1), pander(v.0.6.3), kableExtra(v.1.3.1), dplyr(v.1.0.0), ngsReports(v.1.2.0), tibble(v.3.0.1), ggplot2(v.3.3.2) and BiocGenerics(v.0.32.0)

loaded via a namespace (and not attached): bitops(v.1.0-6), matrixStats(v.0.57.0), lubridate(v.1.7.9.2), webshot(v.0.5.2), RColorBrewer(v.1.1-2), httr(v.1.4.2), GenomeInfoDb(v.1.22.1), tools(v.3.6.1), backports(v.1.2.0), R6(v.2.5.0), DT(v.0.17), lazyeval(v.0.2.2), colorspace(v.1.4-1), withr(v.2.3.0), tidyselect(v.1.1.0), compiler(v.3.6.1), cli(v.2.2.0), rvest(v.0.3.6), Biobase(v.2.46.0), flashClust(v.1.01-2), xml2(v.1.3.2), DelayedArray(v.0.12.3), plotly(v.4.9.3), ggdendro(v.0.1.22), labeling(v.0.4.2), checkmate(v.2.0.0), digest(v.0.6.25), Rsamtools(v.2.2.3), rmarkdown(v.2.6), XVector(v.0.26.0), jpeg(v.0.1-8.1), pkgconfig(v.2.0.3), htmltools(v.0.5.0), highr(v.0.8), FactoMineR(v.2.4), htmlwidgets(v.1.5.3), rlang(v.0.4.11), rstudioapi(v.0.13), farver(v.2.0.3), generics(v.0.1.0), zoo(v.1.8-8), hwriter(v.1.3.2), jsonlite(v.1.7.1), crosstalk(v.1.1.0.1), BiocParallel(v.1.20.1), RCurl(v.1.98-1.2), GenomeInfoDbData(v.1.2.2), leaps(v.3.1), Matrix(v.1.2-18), fansi(v.0.4.1), Rcpp(v.1.0.5), munsell(v.0.5.0), S4Vectors(v.0.24.4), lifecycle(v.0.2.0), scatterplot3d(v.0.3-41), stringi(v.1.4.6), yaml(v.2.2.1), MASS(v.7.3-51.6), SummarizedExperiment(v.1.16.1), zlibbioc(v.1.32.0), plyr(v.1.8.6), grid(v.3.6.1), ggrepel(v.0.9.0), crayon(v.1.3.4), lattice(v.0.20-41), Biostrings(v.2.54.0), hms(v.0.5.3), knitr(v.1.29), pillar(v.1.4.7), GenomicRanges(v.1.38.0), reshape2(v.1.4.4), stats4(v.3.6.1), glue(v.1.4.1), evaluate(v.0.14), ShortRead(v.1.44.3), latticeExtra(v.0.6-29), data.table(v.1.13.6), vctrs(v.0.3.1), png(v.0.1-7), gtable(v.0.3.0), purrr(v.0.3.4), tidyr(v.1.1.2), assertthat(v.0.2.1), xfun(v.0.15), viridisLite(v.0.3.0), truncnorm(v.1.0-8), GenomicAlignments(v.1.22.1), IRanges(v.2.20.2), cluster(v.2.1.0) and ellipsis(v.0.3.1)